similar to: random forest regression

Hi all, I have a dataset where each point is assigned to a class A, B, C, or D. Each point is also assigned to a study site. Each study site is coded with a number ranging between 1-100. This information is stored in the vector studySites. I want to run randomForests using stratified sampling, so I chose the option strata = factor(studySites) But I am not sure how to control the number of

"classwt" in the current version of the randomForest package doesn't work too well. (It's what was in version 3.x of the original Fortran code by Breiman and Cutler, not the one in the new Fortran code.) I'd advise against using it. "sampsize" and "strata" can be use in conjunction. If "strata" is not specified, the class labels will be used.

Hi all, Had struggled in getting "Strata" in randomForest to work on this. Can I get randomForest for each of its TREE, to get ALL sample from some strata to build tree, while leaving some strata TOTALLY untouched as oob? e.g. in below, how I can tell RF to, - for tree 1 in the forest, to use only Site A and B to build the tree, while using the WHOLE Site C data for the oob error

Sorry for the repost, but I've really been looking, and can't find any syntax direction on this issue... Just browsing the documentation, and searching the list came up short... I have some unbalanced data and was wondering if, in a "0" v "1" classification forest, some combo of these options might yield better predictions when the proportion of one class is low (less

Hello there, I am working on an extremely unbalanced two class classification problems. I wanna use "classwt" with "down sampling" together. By checking the rfNews() in R, it looks that classwt is not working yet. Then I looked at the software from Salford. I did not find the down sampling option. I am wondering if you have any experience to deal with this problem. Do you

Dear all, I need to do a Manova but I have an unbalanced design. I have morphological measurements similar to the iris dataset, but I don't have the same number of measurements for all species. Does anyone know a procedure to do Manova with this kind of input in R? Thank you very much, Naiara. -------------------------------------------- Naiara S. Pinto Ecology, Evolution and Behavior 1

Dear all, I would like to use a tree regression method to analyze my dataset. I am interested in the fact that random forests creates in-bag and out-of-bag datasets, but I also need an estimate of support for each split. That seems hard to do in random forests since each tree is grown using a subset of the predictor variables. I was thinking of setting mtry = number of predictor variables,

Hi all, I need some help using read.ftable to read a contingency table. My columns are organized as follows: order--family--species--location--number of individuals I couldn't figure out how to change the data on my text file to be imported into R; and after you do that, is it possible to convert the table into a data frame? Any tips would be greatly appreciatted! Thanks a lot, Naiara.

Hello all, I am trying to use polr (the ordered logistic model from MASS) but I am getting the following error message: Error in if (all(pr > 0)) -sum(wt * log(pr)) else Inf : missing value where TRUE/FALSE needed My response variable is a factor with 3 levels and I have 2 independent variables. I am not sure if I guessed the starting parameters right, which I imagine could be a source of

Hello all, I am importing data from a txt file and try to get a histogram, I get the message: "Error in hist: 'x' must be numeric". When I use mode R returns "List". However when I use srt I get: `data.frame': 456 obs. of 1 variable: $ V1: num 0.6344 0.4516 0.0968 0.7634 0.7957 ... My file consists of one column only (no headers) and I can't figure out why

This is a follow-up to a query that was posted regarding some problems that emerge when running anova analyses for cox models, posted by Mathias Gondan: Matthias Gondan wrote: >* Dear List,*>**>* I have tried a stratified Cox Regression, it is working fine, except for*>* the "Anova"-Tests:*>**>* Here the commands (should work out of the box):*>**>*

Hi! I am dealing with random forest using R. Is there a way to sample a fixed no.of rows from a dataset for use with different trees in random Forest. To be more clear, my data set contains 1500 rows, and I am growing 500 trees in Random Forest Is it possible to sample only 500 rows of data from the data set and use it for different trees in the forest. I mean each tree of the forest should use

Hello, I am new to R, and am having trouble getting the output I want from a stratified bootstrap. I didn't recieve a reply the first time I posted this question so I have tried to make it more clear. My data frame (denboot) is set up as follows: SITE cswa parea treat 1 BeanA 3 1.20 m 2 BeanBC 3 1.05 m 3 BeanD 1 0.93 m 4 BlackB 1 1.01

Dear List, I have tried a stratified Cox Regression, it is working fine, except for the "Anova"-Tests: Here the commands (should work out of the box): library(survival) d = colon[colon$etype==2, ] m = coxph(Surv(time, status) ~ strata(sex) + rx, data=d) summary(m) # Printout ok anova(m, test='Chisq') This is the output of the anova command: > Analysis of Deviance Table

>Hello, I am hoping for assistance in regards to examining the contribution of stratified variables in a cox regression. A previous post by Terry Therneau noted that "That is the point of a strata; you are declaring a variable to NOT be proportional hazards, and thus there is no single "hazard ratio" that describes it". Given this purpose of stratification, in the

Dear WizaRds, Working through sampling theory, I tried to comprehend the concept of stratification and apply it with Survey to a small example. My question is more of theoretic nature, so I apologize if this does not fully fit this board's intention, but I have come to a complete stop in my efforts and need an expert to help me along. Please help: age<-matrix(c(rep(1,5), rep(2,3),

Dear WizaRds, having met some of you in person in Vienna, I think even more fondly of this community and hope to continue on this route. It was great talking with you and learning from you. Thank you. I am trying to work through an artificial example in post stratification. This is my dataset: library(survey) age <- data.frame(id=1:8, stratum=rep(

Good afternoon! I'm trying to use the Survey package for a stratified sample which has 4 criteria on which the stratification is based. I would like to get the corrected weights and for every element i get a weight of 1 E.g: tipping design <- svydesign (id=~1, strata= ~regiune + size_loc + age_rec_hhh + size_hh, data= tabel) and then weights(design) gives

-------------------------------------------------- From: "Ahoussou Sylvie" <sylvie.ahoussou at antilles.inra.fr> Sent: Friday, September 12, 2008 9:48 AM To: "Thomas Lumley" <tlumley at u.washington.edu> Subject: Re: [R] Complex sampling survey _ Use of survey package > Thanks for your answer > > I think I made a mistake when I recopied the 5 first rows of

I am unable to get the basehaz function to apply a proportional hazards model to a new data frame. I replicated my specific situation with the example for coxph in the help, where I changed the x value of the first record from 0 to 1. Is there something incorrect in the syntax that I am using? Thanks in advance! test1 <- list(time= c(4, 3,1,1,2,2,3), status=c(1,NA,1,0,1,1,0),